I think I got a little closer to this mystery.
In between the copying of my first and my second site, I applied some changes to the settings in my FTP-tool; Total Commander in the "FTP tab":
I changed the Default Transfer mode from "Default" to "Automatic", and it actually helped speed up the copying.
But comparing the file sizes for files on my laptop and the size of the same files copied to the server revealed differences in size. The server files where sometimes smaller! (nasty!)
It turned out to be because of this change in settings. When resetting the parameter, copied files would again have the same size as the source.
Now I am in the midst of comparing/copying all the files up again.
So far, I copied all the files, but the problem remains... Hm...
I'll be back when/if I discover the problem...
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